The passenger - one of 75 on board - was cleared by the FBI at Jacksonville International Airport and permitted to continue on the flight to Colombia, the Transportation Security Administration said.
Despite its safe conclusion, the tense situation that arose from diverting a passenger jet after takeoff because of security fears was unlikely to ease the anxiety of the American flying public after the Christmas Day bombing attempt. The government was expected to investigate how the passenger was allowed to board the plane before he was positively deemed safe.
An airline is not supposed to issue a boarding pass to a person on the government's no-fly list.
It was not immediately clear whether the passenger, who was not identified, went through additional screening in Newark before boarding the plane.
The government is rolling out a new program designed to reduce instances of passengers being mistaken for someone on the terror watch lists.
Currently, when airlines check the lists, they do not have any information other than the names on the list. Some airlines have already moved to the new program, called Secure Flight. All domestic carriers are expected to move to the new program by March.
Homeland Security Secretary Janet Napolitano told lawmakers recently that two carriers she did not identify publicly will not meet that deadline. She said the carriers would be a month or two late.
Continental refused to discuss any aspect of Secure Flight, including whether the carrier was one of the two that would be late to adopt the program.
The government system will include more details about the passenger in question, including the passenger's gender, birth date and full name as it appears on the government identification.
